1 CHANGES IN APE VERSION 2.4-1
6 o rtree() and rcoal() now accept a numeric vector for the 'br'
9 o vcv() is a new generic function with methods for the classes "phylo"
10 and "corPhyl" so that it is possible to calculate the var-cov matrix
11 for "transformation models". vcv.phylo() can still be used for trees
12 of class "phylo"; its argument 'cor' has been renamed 'corr'.
17 o bind.tree() failed when 'y' had no root edge.
19 o read.nexus() shuffled tip labels when the trees have no branch
20 lengths and there is a TRANSLATE block.
22 o read.nexus() does not try to translate node labels if there is a
23 translation table in the NEXUS file. See ?read.nexus for a
24 clarification on this behaviour.
26 o plot.multiPhylo() crashed R when plotting a list of trees with
27 compressed tip labels.
29 o write.nexus() did not translate the taxa names when asked for.
31 o plot.phylo(type = "fan") did not rotate the tip labels correctly
32 when the tree has branch lengths.
34 o ace(type = "continuous", method = "ML") now avoids sigma² being
35 negative (which resulted in an error).
39 CHANGES IN APE VERSION 2.4
44 o base.freq() has a new option 'freq' to return the counts; the
45 default is still to return the proportions.
50 o seg.sites() did not handle ambiguous nucleotides correctly: they
53 o plot(phy, root.edge = TRUE) failed if there was no $root.edge in
54 the tree: the argument is now ignored.
56 o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet
62 o Trying to plot a tree with a single tip now returns NULL with a
63 warning (it returned an error previously).
65 o The way lines representing nodes are coloured in phylograms has
66 been modified (as well as their widths and types) following some
67 users' request; this is only for dichotomous nodes.
69 o The argument 'adj' in [node][tip][edge]labels() now works when
70 using 'pie' or 'thermo'.
72 o A more informative message error is now returned by dist.dna() when
73 'model' is badly specified (partial matching of this argument is
76 o Deprecated functions are now listed in a help page: see
77 help("ape-defunct") with the quotes.
82 o The functions heterozygosity, nuc.div, theta.h, theta.k and
83 theta.s have been moved from ape to pegas.
85 o The functions mlphylo, DNAmodel and sh.test have been removed.
89 CHANGES IN APE VERSION 2.3-3
94 o add.scale.bar() always drew a horizontal bar.
96 o zoom() shuffled tips with unrooted trees.
98 o write.nexus() failed to write correctly trees with a "TipLabel"
101 o rcoal() failed to compute branch lengths with very large n.
103 o A small bug was fixed in compar.cheverud() (thanks to Michael
106 o seg.sites() failed when passing a vector.
108 o drop.tip() sometimes shuffled tip labels.
110 o root() shuffled node labels with 'resolve.root = TRUE'.
114 CHANGES IN APE VERSION 2.3-2
119 o all.equal.phylo() did not compare unrooted trees correctly.
121 o dist.topo(... method = "PH85") did not treat unrooted trees
122 correctly (thanks to Tim Wallstrom for the fix).
124 o root() sometimes failed to test for the monophyly of the
127 o extract.clade() sometimes included too many edges.
129 o vcv.phylo() did not work correctly when the tree is in
132 o nj() did not handle correctly distance matrices with many 0's.
133 The code has also been significantly improved: 7, 70, 160 times
134 faster with n = 100, 500, 1000, respectively.
138 CHANGES IN APE VERSION 2.3-1
143 o The new function is.monophyletic tests the monophyly of a group.
145 o There is now a c() method for lists of class "DNAbin".
147 o yule.cov() now fits the null model, and its help page has been
148 corrected with respect to this change.
150 o drop.tip() has a new option 'rooted' to force (or not) a tree
151 to be treated as (un)rooted.
156 o dist.gene() failed on most occasions with the default
157 pairwise.deletion = FALSE.
159 o read.tree() failed to read correctly the tree name(s).
161 o boot.phylo() now treats correctly data frames.
163 o del.gaps() did not copy the rownames of a matrix.
165 o A small bug was fixed in CDAM.global().
167 o ace() failed with large data sets. Thanks to Rich FitzJohn for
168 the fix. With other improvements, this function is now about 6
171 o write.tree() failed with objects of class "multiPhylo".
173 o drop.tip(, subtree = TRUE) sometimes shuffled tip labels.
178 o [.multiPhylo and [.DNAbin now respect the original class.
180 o Instances of the form class(phy) == "phylo" have been replaced
181 by inherits(phy, "phylo").
183 o rcoal() is now faster.
188 o klastorin() has been removed.
192 CHANGES IN APE VERSION 2.3
197 o The new functions CADM.global and CADM.post, contributed by
198 Pierre Legendre, test the congruence among several distance
201 o The new function yule.time fits a user-defined time-dependent
202 Yule model by maximum likelihood.
204 o The new function makeNodeLabel creates and/or modifies node
205 labels in a flexible way.
207 o read.tree() and write.tree() have been modified so that they can
208 handle individual tree names.
210 o plot.phylo() has a new argument 'edge.lty' that specifies the
211 types of lines used for the edges (plain, dotted, dashed, ...)
213 o phymltest() has been updated to work with PhyML 3.0.1.
218 o drop.tip() shuffled tip labels in some cases.
220 o drop.tip() did not handle node.label correctly.
222 o is.ultrametric() now checks the ordering of the edge matrix.
224 o ace() sometimes returned negative values of likelihoods of
225 ancestral states (thanks to Dan Rabosky for solving this long
231 o The data set xenarthra has been removed.
235 CHANGES IN APE VERSION 2.2-4
239 o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
240 now fixed. (Thanks to Peter Wragg for the fix!)
242 o A warning message occurred for no reason with ace(method="GLS").
247 o There is now a general help page displayed with '?ape'.
251 CHANGES IN APE VERSION 2.2-3
256 o The new function extract.clade extracts a clade from a tree by
257 specifying a node number or label.
259 o fastme.bal() has two new options 'spr' and 'tbr' to perform tree
260 operations of the same names.
262 o dist.dna() can now return the number of site differences by
263 specifying model="N".
268 o chronopl() did not work with CV = TRUE.
270 o read.nexus() did not work correctly in some situations (trees on
271 multiple lines with different numbers of lines and/or with
272 comments inserted within the trees).
274 o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly
275 the number of lineages with non-binary trees.
280 o ape has now a namespace.
282 o drop.tip() has been improved: it should be much faster and work
283 better in some cases (e.g., see the example in ?zoom).
287 CHANGES IN APE VERSION 2.2-2
292 o dist.gene() has been substantially improved and gains an option
295 o cbind.DNAbin() has a new option 'fill.with.gaps' and is now
301 o prop.part() failed with a single tree with the default option
302 'check.labels = TRUE'.
304 o summary.DNAbin() failed to display correctly the summary of
305 sequence lengths with lists of sequences of 10,000 bases or more
306 (because summary.default uses 4 significant digits by default).
308 o read.nexus() failed to read a file with a single tree with line
309 breaks in the Newick string.
311 o del.gaps() returned a list of empty sequences when there were no
317 o phymltest() has been updated for PhyML 3.0 and gains an option
318 'append', whereas the option 'path2exec' has been removed.
320 o rbind.DNAbin() and cbind.DNAbin() now accept a single matrix
321 which is returned unchanged (instead of an error).
323 o The data sets bird.orders and bird.families are now stored as
324 Newick strings; i.e., the command data(bird.orders) calls
329 CHANGES IN APE VERSION 2.2-1
334 o The new function makeLabel() helps to modify labels of trees,
335 lists of trees, or DNA sequences, with several utilities to
336 truncate and/or make them unique, substituting some
337 characters, and so on.
339 o The new function del.gaps() removes insertion gaps ("-") in a
340 set of DNA sequences.
342 o read.dna() can now read Clustal files (*.aln).
347 o root() failed with 'resolve.root = TRUE' when the root was
348 already the specified root.
350 o Several bugs were fixed in mlphylo().
352 o collapsed.singles() did not propagate the 'Nnode' and
353 'node.labels' elements (thanks to Elizabeth Purdom for the fix).
355 o read.nexus() failed to remove correctly the comments within
358 o read.nexus() failed to read a file with a single tree and no
359 translation of tip labels.
361 o read.nexus() failed to place correctly tip labels when reading
362 a single tree with no edge lengths.
364 o A bug was fixed in sh.test().
369 o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
372 o The option 'check.labels' of consensus() and prop.part() is now
375 o write.dna() now does not truncate names to 10 characters with
380 CHANGES IN APE VERSION 2.2
385 o Four new functions have been written by Damien de Vienne for the
386 graphical exploration of large trees (cophyloplot, subtrees,
387 subtreeplot), and to return the graphical coordinates of tree
390 o The new functions corPagel and corBlomberg implement the Pagel's
391 "lambda" and Blomberg et al.'s "ACDC" correlation structures.
393 o chronopl() has been improved and gains several options: see its
394 help page for details.
396 o boot.phylo() has now an option 'trees' to possibly return the
397 bootstraped trees (the default is FALSE).
399 o prop.part() has been improved and should now be faster in all
405 o read.dna() failed if "?" occurred in the first 10 sites of the
408 o The x/y aspect of the plot is now respected when plotting a
409 circular tree (type = "r" or "f").
411 o Drawing the tip labels sometimes failed when plotting circular
414 o zoom() failed when tip labels were used instead of their numbers
415 (thanks to Yan Wong for the fix).
417 o drop.tip() failed with some trees (fixed by Yan Wong).
419 o seg.sites() failed with a list.
421 o consensus() failed in some cases. The function has been improved
422 as well and is faster.
426 CHANGES IN APE VERSION 2.1-3
431 o A bug in read.nexus() made the Windows R-GUI crash.
433 o An error was fixed in the computation of ancestral character
434 states by generalized least squares in ace().
436 o di2multi() did not modify node labels correctly.
438 o multi2di() failed if the tree had its attribute "order" set to
443 CHANGES IN APE VERSION 2.1-2
448 o There three new methods for the "multiPhylo" class: str, $,
451 o root() gains the options 'node' and 'resolve.root'
452 (FALSE by default) as well as its code being improved.
454 o mltt.plot() has now an option 'log' used in the same way
455 than in plot.default().
460 o mltt.plot() failed to display the legend with an unnamed
463 o nodelabels() with pies now correcly uses the argument
464 'cex' to draw symbols of different sizes (which has
465 worked already for thermometers).
467 o read.nexus() generally failed to read very big files.
472 o The argument 'family' of compar.gee() can now be a function
473 as well as a character string.
475 o read.tree() and read.nexus() now return an unnamed list if
478 o read.nexus() now returns a modified object of class "multiPhylo"
479 when there is a TRANSLATE block in the NEXUS file: the individual
480 trees have no 'tip.label' vector, but the list has a 'TipLabel'
481 attribute. The new methods '$' and '[[' set these elements
482 correctly when extracting trees.
486 CHANGES IN APE VERSION 2.1-1
491 o The new function rmtree generates lists of random trees.
493 o rcoal() now generates a genuine coalescent tree by default
494 (thanks to Vladimir Minin for the code).
499 o nuc.div() returned an incorrect value with the default
500 pairwise.deletion = FALSE.
505 o The internal codes of bionj(), fastme.bal(), and fastme.ols()
506 have been improved so that they are stabler and faster.
508 o R packages used by ape are now loaded silently; lattice and gee
509 are loaded only when needed.
513 CHANGES IN APE VERSION 2.1
518 o The new function identify.phylo identifies clades on a plotted
519 tree using the mouse.
521 o It is now possible to subset a list of trees (object of class
522 "multiPhylo") with "[" while keeping its class correct.
524 o The new function as.DNAbin.alignment converts DNA sequences
525 stored in the "alignment" format of the package seqinr into
526 an object of class "DNAbin".
528 o The new function weight.taxo2 helps to build similarity matrices
529 given two taxonomic levels (usually called by other functions).
531 o write.tree() can now take a list of trees (class "multiPhylo")
532 as its main argument.
534 o plot.correlogram() and plot.correlogramList() have been
535 improved, and gain several options (see the help page for
536 details). A legend is now plotted by default.
541 o dist.dna() returned some incorrect values with `model = "JC69"'
542 and `pairwise.deletion = TRUE'. This affected only the
543 distances involving sequences with missing values. (Thanks
544 to Bruno Toupance for digging this bug out.)
546 o write.tree() failed with some trees: this is fixed by removing
547 the `multi.line' option (trees are now always printed on a
550 o read.nexus() did not correctly detect trees with multiple root
551 edges (see OTHER CHANGES).
556 o The code of mlphylo() has been almost entirely rewritten, and
557 should be much stabler. The options have been also greatly
558 simplified (see ?mlphylo and ?DNAmodel for details).
560 o The internal function nTips has been renamed klastorin_nTips.
562 o The code of is.ultrametric() contained redundancies and has
565 o The code of Moran.I() and of correlogram.formula() have been
568 o read.tree() and read.nexus() now return an error when trying to
569 read a tree with multiple root edges (see BUG FIXES). The
570 correction applied in previous version did not work in all
573 o The class c("multi.tree", "phylo") has been renamed
579 o There is now a vignette in ape: see vignette("MoranI", "ape").
584 o as.matching() and as.phylo.matching() do not support branch
587 o correlogram.phylo() and discrete.dist() have been removed.
591 CHANGES IN APE VERSION 2.0-2
596 o The new function matexpo computes the exponential of a square
599 o The new function unique.multi.tree removes duplicate trees from
602 o yule() has a new option `use.root.edge = FALSE' that specifies
603 to ignore, by default, the root edge of the tree if it exists.
608 o which.edge() failed when the index of a single terminal edge was
611 o In diversi.time(), the values returned for model C were
614 o A bug was fixed in yule() that affected the calculation of the
615 likelihood in the presence of ties in the branching times.
617 o There was a bug in the C function mat_expo4x4 affecting the
618 calculations of the transition probabilities for models HKY and
621 o A small bug was fixed in as.matrix.DNAbin (thanks to James
624 o rtree() did not `shuffle' the tip labels by default, so only a
625 limited number of labelled topologies could be generated.
629 CHANGES IN APE VERSION 2.0-1
634 o The three new functions bionj, fastme.ols, and fastme.bal
635 perform phylogeny estimation by the BIONJ and fastME methods in
636 OLS and balanced versions. This is a port to R of previous
637 previous programs done by Vincent Lefort.
639 o The new function chronoMPL performs molecular dating with the
640 mean path lengths method of Britton et al. (2002, Mol. Phyl.
643 o The new function rotate, contributed by Christoph Heibl, swaps
644 two clades connected to the same node. It works also with
645 multichotomous nodes.
647 o The new `method' as.matrix.DNAbin() may be used to convert
648 easily DNA sequences stored in a list into a matrix while
649 keeping the names and the class.
654 o chronopl() failed when some branch lengths were equal to zero:
655 an error message is now returned.
657 o di2multi() failed when there was a series of consecutive edges
662 CHANGES IN APE VERSION 1.10-2
667 o plot.phylo() can now plot circular trees: the option is type =
668 "fan" or type = "f" (to avoid the ambiguity with type = "c").
670 o prop.part() has a new option `check.labels = FALSE' which allows
671 to considerably speed-up the calculations of bipartitions. As a
672 consequence, calculations of bootstrap values with boot.phylo()
673 should be much faster.
678 o read.GenBank() did not return correctly the list of species as
679 from ape 1.10: this is fixed in this version
681 o Applying as.phylo() on a tree of class "phylo" failed: the
682 object is now returned unchanged.
686 CHANGES IN APE VERSION 1.10-1
691 o The three new functions Ntip, Nnode, and Nedge return, for a
692 given tree, the number of tips, nodes, or edges, respectively.
697 o read.nexus() did not set correctly the class of the returned
698 object when reading multiple trees.
700 o mllt.plot() failed with objects of class c("multi.tree",
703 o unroot() did not work correctly in most cases.
705 o reorder.phylo() made R freeze in some occasions.
707 o Plotting a tree in pruningwise order failed.
709 o When plotting an unrooted tree, the tip labels where not all
710 correctly positioned if the option `cex' was used.
714 CHANGES IN APE VERSION 1.10
719 o Five new `method' functions have been introduced to manipulate
720 DNA sequences in binary format (see below).
722 o Three new functions have been introduced to convert between the
723 new binary and the character formats.
725 o The new function as.alignment converts DNA sequences stored as
726 single characters into the class "alignment" used by the package
729 o read.dna() and read.GenBank() have a new argument `as.character'
730 controlling whether the sequences are returned in binary format
736 o root() failed when the tree had node labels: this is fixed.
738 o plot.phylo() did not correctly set the limits on the y-axis with
739 the default setting: this is fixed.
741 o dist.dna() returned a wrong result for the LogDet, paralinear,
742 and BH87 models with `pairwise.deletion = TRUE'.
747 o DNA sequences are now internally stored in a binary format. See
748 the document "A Bit-Level Coding Scheme for Nucleotides" for the
749 details. Most functions analyzing DNA functions have been
750 modified accordingly and are now much faster (dist.dna is now
751 ca. 60 times faster).
755 CHANGES IN APE VERSION 1.9-4
760 o A bug was fixed in edgelabels().
762 o as.phylo.hclust() did not work correctly when the object of
763 class "hclust" has its labels set to NULL: the returned tree has
764 now its tip labels set to "1", "2", ...
766 o consensus could fail if some tip labels are a subset of others
767 (e.g., "a" and "a_1"): this is now fixed.
769 o mlphylo() failed in most cases if some branch lengths of the
770 initial tree were greater than one: an error message is now
773 o mlphylo() failed in most cases when estimating the proportion of
774 invariants: this is fixed.
778 CHANGES IN APE VERSION 1.9-3
783 o The new function edgelabels adds labels on the edge of the tree
784 in the same way than nodelabels or tiplabels.
789 o multi2di() did not handle correctly branch lengths with the
790 default option `random = TRUE': this is now fixed.
792 o A bug was fixed in nuc.div() when using pairwise deletions.
794 o A bug occurred in the analysis of bipartitions with large
795 numbers of large trees, with consequences on prop.part,
796 prop.clades, and boot.phylo.
798 o The calculation of the Billera-Holmes-Vogtmann distance in
799 dist.topo was wrong: this has been fixed.
803 CHANGES IN APE VERSION 1.9-2
808 o The new function ladderize reorganizes the internal structure of
809 a tree to plot them left- or right-ladderized.
811 o The new function dist.nodes computes the patristic distances
812 between all nodes, internal and terminal, of a tree. It replaces
813 the option `full = TRUE' of cophenetic.phylo (see below).
818 o A bug was fixed in old2new.phylo().
820 o Some bugs were fixed in chronopl().
822 o The edge colours were not correctly displayed by plot.phylo
823 (thank you to Li-San Wang for the fix).
825 o cophenetic.phylo() failed with multichotomous trees: this is
831 o read.dna() now returns the sequences in a matrix if they are
832 aligned (interleaved or sequential format). Sequences in FASTA
833 format are still returned in a list.
835 o The option `full' of cophenetic.phylo() has been removed because
836 it could not be used from the generic.
841 o rotate() has been removed; this function did not work correctly
846 CHANGES IN APE VERSION 1.9-1
851 o Trees with a single tip were not read correctly in R as the
852 element `Nnode' was not set: this is fixed.
854 o unroot() did not set correctly the number of nodes of the
855 unrooted tree in most cases.
857 o read.GenBank() failed when fetching very long sequences,
858 particularly of the BX-series.
860 o A bug was introduced in read.tree() with ape 1.9: it has been
865 CHANGES IN APE VERSION 1.9
870 o There are two new print `methods' for trees of class "phylo" and
871 lists of trees of class "multi.tree", so that they are now
872 displayed in a compact and informative way.
874 o There are two new functions, old2new.phylo and new2old.phylo,
875 for converting between the old and new coding of the class
878 o dist.dna() has three new models: Barry and Hartigan ("BH87"),
879 LogDet ("logdet"), and paralinear ("paralin").
881 o compute.brlen() has been extended: several methods are now
882 available to compute branch lengths.
884 o write.dna() can now handle matrices as well as lists.
889 o cophenetic.phylo() sometimes returned a wrong result with
890 multichotomous trees: this is fixed.
892 o rotate() failed when a single tip was specified: the tree is now
895 o ace() did not return the correct index matrix with custom
896 models: this is fixed.
898 o multi2di() did not work correctly when resolving multichotomies
899 randomly: the topology was always the same, only the arrangement
900 of clades was randomized: this is fixed. This function now
901 accepts trees with no branch lengths.
903 o The output of diversi.gof() was blurred by useless prints when a
904 user distribution was specified. This has been corrected, and
905 the help page of this function has been expanded.
910 o The internal structure of the class "phylo" has been changed:
911 see the document "Definition of Formats for Coding Phylogenetic
912 Trees in R" for the details. In addition, the code of most
913 functions has been improved.
915 o Several functions have been improved by replacing some R codes
916 by C codes: pic, plot.phylo, and reorder.phylo.
918 o There is now a citation information: see citation("ape") in R.
920 o write.tree() now does not add extra 0's to branch lengths so
921 that 1.23 is printed "1.23" by default, not "1.2300000000".
923 o The syntax of bind.tree() has been simplified. This function now
924 accepts trees with no branch lengths, and handles correctly node
927 o The option `as.numeric' of mrca() has been removed.
929 o The unused options `format' and `rooted' of read.tree() have
932 o The unused option `format' of write.tree() has been removed.
934 o The use of node.depth() has been simplified.
938 CHANGES IN APE VERSION 1.8-5
943 o Two new functions read.nexus.data() and write.nexus.data(),
944 contributed by Johan Nylander, allow to read and write molecular
945 sequences in NEXUS files.
947 o The new function reorder.phylo() reorders the internal structure
948 of a tree of class "phylo". It is used as the generic, e.g.,
951 o read.tree() and read.nexus() can now read trees with a single
954 o The new data set `cynipids' supplies a set of protein sequences
960 o The code of all.equal.phylo() has been completely rewritten
961 (thanks to Benoît Durand) which fixes several bugs.
963 o read.tree() and read.nexus() now checks the labels of the tree
964 to remove or substitute any characters that are illegal in the
965 Newick format (parentheses, etc.)
967 o A negative P-value could be returned by mantel.test(): this is
972 CHANGES IN APE VERSION 1.8-4
977 o The new function sh.test() computes the Shimodaira-
980 o The new function collapse.singles() removes the nodes with a
981 single descendant from a tree.
983 o plot.phylo() has a new argument `tip.color' to specify the
986 o mlphylo() has now an option `quiet' to control the display of
987 the progress of the analysis (the default is FALSE).
992 o read.dna() did not read correctly sequences in sequential format
993 with leading alignment gaps "-": this is fixed.
995 o ace() returned a list with no class so that the generic
996 functions (anova, logLik, ...) could not be used directly. This
997 is fixed as ace() now returns an object of class "ace".
999 o anova.ace() had a small bug when computing the number of degrees
1000 of freedom: this is fixed.
1002 o mlphylo() did not work when the sequences were in a matrix or
1003 a data frame: this is fixed.
1005 o rtree() did not work correctly when trying to simulate an
1006 unrooted tree with two tips: an error message is now issued.
1011 o The algorithm of rtree() has been changed: it is now about 40,
1012 100, and 130 times faster for 10, 100, and 1000 tips,
1017 CHANGES IN APE VERSION 1.8-3
1022 o There are four new `method' functions to be used with the
1023 results of ace(): logLik(), deviance(), AIC(), and anova().
1025 o The plot method of phymltest has two new arguments: `main' to
1026 change the title, and `col' to control the colour of the
1027 segments showing the AIC values.
1029 o ace() has a new argument `ip' that gives the initial values used
1030 in the ML estimation with discrete characters (see the examples
1031 in ?ace). This function now returns a matrix giving the indices
1032 of the estimated rates when analysing discrete characters.
1034 o nodelabels() and tiplabels() have a new argument `pie' to
1035 represent proportions, with any number of categories, as
1036 piecharts. The use of the option `thermo' has been improved:
1037 there is now no limitation on the number of categories.
1042 o mlphylo() did not work with more than two partitions: this is
1045 o root() failed if the proposed outgroup was already an outgroup
1046 in the tree: this is fixed.
1048 o The `col' argument in nodelabels() and tiplabels() was not
1049 correctly passed when `text' was used: this is fixed.
1051 o Two bugs were fixed in mlphylo(): parameters were not always
1052 correctly output, and the estimation failed in some cases.
1054 o plot.phylo() was stuck when given a tree with a single tip: this
1055 is fixed and a message error is now returned.
1057 o An error was corrected in the help page of gammaStat regarding
1058 the calculation of P-values.
1060 o Using gls() could crash R when the number of species in the tree
1061 and in the variables were different: this is fixed.
1065 CHANGES IN APE VERSION 1.8-2
1070 o The new function mlphylo() fits a phylogenetic tree by maximum
1071 likelihood from DNA sequences. Its companion function DNAmodel()
1072 is used to define the substitution model which may include
1073 partitioning. There are methods for logLik(), deviance(), and
1074 AIC(), and the summary() method has been extended to display in
1075 a friendly way the results of this model fitting. Currently, the
1076 functionality is limited to estimating the substitution and
1077 associated parameters and computing the likelihood.
1079 o The new function drop1.compar.gee (used as, e.g., drop1(m))
1080 tests for single effects in GEE-based comparative method. A
1081 warning message is printed if there is not enough degrees of
1087 o An error message was sometimes issued by plot.multi.tree(),
1088 though with no consequence.
1092 CHANGES IN APE VERSION 1.8-1
1097 o There is a new plot method for lists of trees (objects of class
1098 "multi.tree"): it calls plot.phylo() internally and is
1099 documented on the same help page.
1104 o A bug was fixed in the C code that analyzes bipartitions: this
1105 has impact on several functions like prop.part, prop.clades,
1106 boot.phylo, or consensus.
1108 o root() did not work correctly when the specified outgroup had
1109 more than one element: this is fixed.
1111 o dist.dna() sometimes returned a warning inappropriately: this
1114 o If the distance object given to nj() had no rownames, nj()
1115 returned a tree with no tip labels: it now returns tips labelled
1116 "1", "2", ..., corresponding to the row numbers.
1121 o nj() has been slightly changed so that tips with a zero distance
1122 are first aggregated with zero-lengthed branches; the usual NJ
1123 procedure is then performed on a distance matrix without 0's.
1127 CHANGES IN APE VERSION 1.8
1132 o The new function chronopl() estimates dates using the penalized
1133 likelihood method by Sanderson (2002; Mol. Biol. Evol., 19:101).
1135 o The new function consensus() calculates the consensus tree of a
1138 o The new function evolve.phylo() simulates the evolution of
1139 continuous characters along a phylogeny under a Brownian model.
1141 o The new plot method for objects of class "ancestral" displays a
1142 tree together with ancestral values, as returned by the above
1145 o The new function as.phylo.formula() returns a phylogeny from a
1146 set of nested taxonomic variables given as a formula.
1148 o The new function read.caic() reads trees in CAIC format.
1150 o The new function tiplabels() allows to add labels to the tips
1151 of a tree using text or plotting symbols in a flexible way.
1153 o The new function unroot() unroots a phylogeny.
1155 o multi2di() has a new option, `random', which specifies whether
1156 to resolve the multichotomies randomly (the default) or not.
1158 o prop.part() now returns an object of class "prop.part" for which
1159 there are print (to display a partition in a more friendly way)
1160 and summary (to extract the numbers) methods.
1162 o plot.phylo() has a new option, `show.tip.label', specifying
1163 whether to print the labels of the tips. The default is TRUE.
1165 o The code of nj() has been replaced by a faster C code: it is now
1166 about 10, 25, and 40 times faster for 50, 100, and 200 taxa,
1169 o write.nexus() now writes whether a tree is rooted or not.
1174 o Two bugs have been fixed in root(): unrooted trees are now
1175 handled corretly, and node labels are now output normally.
1177 o A bug was fixed in phymltest(): the executable couldn't be found
1180 o Three bug have been fixed in ace(): computing the likelihood of
1181 ancestral states of discrete characters failed, custom models
1182 did not work, and the function failed with a null gradient (a
1183 warning message is now returned; this latter bug was also
1184 present in yule.cov() as well and is now fixed).
1186 o pic() hanged out when missing data were present: a message error
1189 o A small bug was fixed in dist.dna() where the gamma correction
1190 was not always correctly dispatched.
1192 o plot.phylo() plotted correctly the root edge only when the tree
1193 was plotted rightwards: this works now for all directions.
1198 o dist.taxo() has been renamed as weight.taxo().
1200 o Various error and warning messages have been improved.
1204 CHANGES IN APE VERSION 1.7
1207 o The new function ace() estimates ancestral character states for
1208 continuous characters (with ML, GLS, and contrasts methods), and
1209 discrete characters (with ML only) for any number of states.
1211 o The new function compar.ou() fits the Ornstein-Uhlenbeck model
1212 of directional evolution for continuous characters. The user
1213 specifies the node(s) of the tree where the character optimum
1216 o The new function is.rooted() tests whether a tree (of class
1219 o The new function rcoal() generates random ultrametric trees with
1220 the possibility to specify the function that generates the
1221 inter-nodes distances.
1223 o The new function mrca() gives for all pairs of tips in a tree
1224 (and optionally nodes too) the most recent common ancestor.
1226 o nodelabels() has a new option `thermo' to plot proportions (up
1227 to three classes) on the nodes of a tree.
1229 o rtree() has been improved: it can now generate rooted or
1230 unrooted trees, and the mathematical function that generates the
1231 branch lengths may be specified by the user. The tip labels may
1232 be given directly in the call to rtree. The limit cases (n = 2,
1233 3) are now handled correctly.
1235 o dist.topo() has a new argument `method' with two choices: "PH85"
1236 for Penny and Henny's method (already available before and now
1237 the default), and "BHV01" for the geometric distance by Billera
1238 et al. (2001, Adv. Appl. Math. 27:733).
1240 o write.tree() has a new option, `digits', which specifies the
1241 number of digits to be printed in the Newick tree. By default
1242 digits = 10. The numbers are now always printed in decimal form
1243 (i.e., 1.0e-1 is now avoided).
1245 o dist.dna() can now compute the raw distances between pairs of
1246 DNA sequences by specifying model = "raw".
1248 o dist.phylo() has a new option `full' to possibly compute the
1249 distances among all tips and nodes of the tree. The default if
1255 o Several bugs were fixed in all.equal.phylo().
1257 o dist.dna() did not handle correctly gaps ("-") in alignments:
1258 they are now considered as missing data.
1260 o rotate() did not work if the tips were not ordered: this is
1263 o mantel.test() returned NA in some special cases: this is fixed
1264 and the function has been improved and is now faster.
1266 o A bug was fixed in diversi.gof() where the calculation of A² was
1269 o cherry() did not work correctly under some OSs (mainly Linux):
1272 o is.binary.tree() has been modified so that it works with both
1273 rooted and unrooted trees.
1275 o The documentation of theta.s() was not correct: this has been
1278 o plot.mst() did not work correctly: this is fixed.
1282 CHANGES IN APE VERSION 1.6
1287 o The new function dist.topo() computes the topological distances
1290 o The new function boot.phylo() performs a bootstrap analysis on
1291 phylogeny estimation.
1293 o The new functions prop.part() and prop.clades() analyse
1294 bipartitions from a series of trees.
1299 o read.GenBank() now uses the EFetch utility of NCBI instead of
1300 the usual Web interface: it is now much faster (e.g., 12 times
1301 faster to retrieve 8 sequences, 37 times for 60 sequences).
1306 o Several bugs were fixed in read.dna().
1308 o Several bugs were fixed in diversi.time().
1310 o is.binary.tree() did not work correctly if the tree has no edge
1311 lengths: this is fixed.
1313 o drop.tip() did not correctly propagated the `node.label' of a
1314 tree: this is fixed.
1318 CHANGES IN APE VERSION 1.5
1323 o Two new functions, as.matching.phylo() and as.phylo.matching(),
1324 convert objects between the classes "phylo" and "matching". The
1325 latter implements the representation of binary trees introduced by
1326 Diaconis and Holmes (1998; PNAS 95:14600). The generic function
1327 as.matching() has been introduced as well.
1329 o Two new functions, multi2di() and di2multi(), allow to resolve
1330 and collapse multichotomies with branches of length zero.
1332 o The new function nuc.div() computes the nucleotide diversity
1333 from a sample a DNA sequences.
1335 o dist.dna() has been completely rewritten with a much faster
1336 (particularly for large data sets) C code. Eight models are
1337 available: JC69, K80, F81, K81, F84, T92, TN93, and GG95 (the
1338 option `method' has been renamed `model'). Computation of variance
1339 is available for all models. A gamma-correction is possible for
1340 JC69, K80, F81, and TN93. There is a new option, pairwise.deletion,
1341 to remove sites with missing data on a pairwise basis. The option
1342 `GCcontent' has been removed.
1344 o read.GenBank() has a new option (species.names) which specifies
1345 whether to return the species names of the organisms in addition
1346 to the accession numbers of the sequences (this is the default
1349 o write.nexus() can now write several trees in the same NEXUS file.
1351 o drop.tip() has a new option `root.edge' that allows to specify the
1352 new root edge if internal branches are trimmed.
1357 o as.phylo.hclust() failed if some labels had parentheses: this
1360 o Several bugs were fixed in all.equal.phylo(). This function now
1361 returns the logical TRUE if the trees are identical but with
1362 different representations (a report was printed previously).
1364 o read.GenBank() did not correctly handle ambiguous base codes:
1370 o birthdeath() now returns an object of class "birthdeath" for
1371 which there is a print method.
1375 CHANGES IN APE VERSION 1.4
1380 o The new function nj() performs phylogeny estimation with the
1381 neighbor-joining method of Saitou and Nei (1987; Mol. Biol.
1384 o The new function which.edge() identifies the edges of a tree
1385 that belong to a group specified as a set of tips.
1387 o The new function as.phylo.phylog() converts an object of class
1388 "phylog" (from the package ade4) into an object of class
1391 o The new function axisPhylo() draws axes on the side of a
1394 o The new function howmanytrees() calculates the number of trees
1395 in different cases and giving a number of tips.
1397 o write.tree() has a new option `multi.line' (TRUE by default) to
1398 write a Newick tree on several lines rather than on a single
1401 o The functionalities of zoom() have been extended. Several
1402 subtrees can be visualized at the same time, and they are marked
1403 on the main tree with colors. The context of the subtrees can be
1404 marked with the option `subtree' (see below).
1406 o drop.tip() has a new option `subtree' (FALSE by default) which
1407 specifies whether to output in the tree how many tips have been
1410 o The arguments of add.scale.bar() have been redefined and have
1411 now default values (see ?add.scale.bar for details). This
1412 function now works even if the plotted tree has no edge length.
1414 o plot.phylo() can now plot radial trees, but this does not take
1415 edge lengths into account.
1417 o In plot.phylo() with `type = "phylogram"', if the values of
1418 `edge.color' and `edge.width' are identical for sister-branches,
1419 they are propagated to the vertical line that link them.
1424 o Repeated calls to as.phylo.hclust() or as.hclust.phylo() made R
1425 crashing. This is fixed.
1427 o In plot.phylo(), the options `edge.color' and `edge.width' are
1428 now properly recycled; their default values are now "black" and
1431 o A bug has been fixed in write.nexus().
1436 o The function node.depth.edgelength() has been removed and
1437 replaced by a C code.
1441 CHANGES IN APE VERSION 1.3-1
1446 o The new function nodelabels() allows to add labels to the nodes
1447 of a tree using text or plotting symbols in a flexible way.
1449 o In plot.phylo() the arguments `x.lim' and `y.lim' can now be two
1450 numeric values specifying the lower and upper limits on the x-
1451 and y-axes. This allows to leave some space on any side of the
1452 tree. If a single value is given, this is taken as the upper
1457 CHANGES IN APE VERSION 1.3
1462 o The new function phymltest() calls the software PHYML and fits
1463 28 models of DNA sequence evolution. There are a print method to
1464 display likelihood and AIC values, a summary method to compute
1465 the hierarchical likelihood ratio tests, and a plot method to
1466 display graphically the AIC values of each model.
1468 o The new function yule.cov() fits the Yule model with covariates,
1469 a model where the speciation rate is affected by several species
1470 traits through a generalized linear model. The parameters are
1471 estimated by maximum likelihood.
1473 o Three new functions, corBrownian(), corGrafen(), and
1474 corMartins(), compute the expected correlation structures among
1475 species given a phylogeny under different models of evolution.
1476 These can be used for GLS comparative phylogenetic methods (see
1477 the examples). There are coef() and corMatrix() methods and an
1478 Initialize.corPhyl() function associated.
1480 o The new function compar.cheverud() implements Cheverud et al.'s
1481 (1985; Evolution 39:1335) phylogenetic comparative method.
1483 o The new function varcomp() estimates variance components; it has
1486 o Two new functions, panel.superpose.correlogram() and
1487 plot.correlogramList(), allow to plot several phylogenetic
1490 o The new function node.leafnumber() computes the number of leaves
1491 of a subtree defined by a particular node.
1493 o The new function node.sons() gets all tags of son nodes from a
1496 o The new function compute.brlen() computes the branch lengths of
1497 a tree according to a specified method.
1499 o plot.phylo() has three new options: "cex" controls the size of
1500 the (tip and node) labels (thus it is no more needed to change
1501 the global graphical parameter), "direction" which allows to
1502 plot the tree rightwards, leftwards, upwards, or downwards, and
1503 "y.lim" which sets the upper limit on the y-axis.
1508 o Some functions which try to match tip labels and names of
1509 additional data (e.g. vector) are likely to fail if there are
1510 typing or syntax errors. If both series of names do not perfectly
1511 match, they are ignored and a warning message is now issued.
1512 These functions are bd.ext, compar.gee, pic. Their help pages
1513 have been clarified on this point.
1517 CHANGES IN APE VERSION 1.2-7
1522 o The new function root() reroots a phylogenetic tree with respect
1523 to a specified outgroup.
1525 o The new function rotate() rotates an internal branch of a tree.
1527 o In plot.phylo(), the new argument "lab4ut" (labels for unrooted
1528 trees) controls the display of the tip labels in unrooted trees.
1529 This display has been greatly improved: the tip labels are now not
1530 expected to overlap with the tree (particularly if lab4ut =
1531 "axial"). In all cases, combining appropriate values of "lab4ut"
1532 and the font size (via "par(cex = )") should result in readable
1533 unrooted trees. See ?plot.phylo for some examples.
1535 o In drop.tip(), the argument `tip' can now be numeric or character.
1540 o drop.tip() did not work correctly with trees with no branch
1541 lengths: this is fixed.
1543 o A bug in plot.phylo(..., type = "unrooted") made some trees being
1544 plotted with some line crossings: this is now fixed.
1548 CHANGES IN APE VERSION 1.2-6
1553 o Six new functions (Moran.I, correlogram.formula, discrete.dist,
1554 correlogram.phylo, dist.taxo, plot.correlogram) have been added
1555 to implement comparative methods with an autocorrelation approach.
1557 o A new data set describing some life history traits of Carnivores
1563 o A fix was made on mcmc.popsize() to conform to R 2.0.0.
1568 o When plotting a tree with plot.phylo(), the new default of the
1569 option `label.offset' is now 0, so the labels are always visible.
1573 CHANGES IN APE VERSION 1.2-5
1578 o The new function bd.ext() fits a birth-death model with combined
1579 phylogenetic and taxonomic data, and estimates the corresponding
1580 speciation and extinction rates.
1585 o The package gee is no more required by ape but only suggested
1586 since only the function compar.gee() calls gee.
1590 CHANGES IN APE VERSION 1.2-4
1595 o Four new functions (mcmc.popsize, extract.popsize, plot.popsize,
1596 and lines.popsize) implementing a new approach for inferring the
1597 demographic history from genealogies using a reversible jump
1598 MCMC have been introduced.
1600 o The unit of time in the skyline plot and in the new plots can
1601 now be chosen to be actual years, rather than substitutions.
1605 CHANGES IN APE VERSION 1.2-3
1610 o The new function rtree() generates a random binary tree with or
1611 without branch lengths.
1613 o Two new functions for drawing lineages-through-time (LTT) plots
1614 are provided: ltt.lines() adds a LTT curve to an existing plot,
1615 and mltt.plot() does a multiple LTT plot giving several trees as
1616 arguments (see `?ltt.plot' for details).
1621 o Some taxon names made R crashing when calling as.phylo.hclust():
1624 o dist.dna() returned an error with two identical DNA sequences
1625 (only using the Jukes-Cantor method returned 0): this is fixed.
1630 o The function dist.phylo() has been re-written using a different
1631 algorithm: it is now about four times faster.
1633 o The code of branching.times() has been improved: it is now about
1638 CHANGES IN APE VERSION 1.2-2
1643 o The new function seg.sites() finds the segregating sites in a
1644 sample of DNA sequences.
1649 o A bug introduced in read.tree() and in read.nexus() with version
1652 o A few errors were corrected and a few examples were added in the
1657 CHANGES IN APE VERSION 1.2-1
1662 o plot.phylo() can now draw the edge of the root of a tree if it
1663 has one (see the new option `root.edge', its default is FALSE).
1668 o A bug was fixed in read.nexus(): files with semicolons inside
1669 comment blocks were not read correctly.
1671 o The behaviour of read.tree() and read.nexus() was corrected so
1672 that tree files with badly represented root edges (e.g., with
1673 an extra pair of parentheses, see the help pages for details)
1674 are now correctly represented in the object of class "phylo";
1675 a warning message is now issued.
1679 CHANGES IN APE VERSION 1.2
1684 o plot.phylo() has been completely re-written and offers several
1685 new functionalities. Three types of trees can now be drawn:
1686 phylogram (as previously), cladogram, and unrooted tree; in
1687 all three types the branch lengths can be drawn using the edge
1688 lengths of the phylogeny or not (e.g., if the latter is absent).
1689 The vertical position of the nodes can be adjusted with two
1690 choices (see option `node.pos'). The code has been re-structured,
1691 and two new functions (potentially useful for developpers) are
1692 documented separately: node.depth.edgelength() and node.depth();
1693 see the respective help pages for details.
1695 o The new function zoom() allows to explore very large trees by
1696 focusing on a small portion of it.
1698 o The new function yule() fits by maximum likelihood the Yule model
1699 (birth-only process) to a phylogenetic tree.
1701 o Support for writing DNA sequences in FASTA format has been
1702 introduced in write.dna() (support for reading sequences in
1703 this format was introduced in read.dna() in version 1.1-2).
1704 The function has been completely re-written, fixing some bugs
1705 (see below); the default behaviour is no more to display the
1706 sequences on the standard output. Several options have been
1707 introduced to control the sequence printing in a flexible
1708 way. The help page has been extended.
1710 o A new data set is included: a supertree of bats in NEXUS format.
1715 o In theta.s(), the default of the option `variance' has
1716 been changed to `FALSE' (as was indicated in the help page).
1718 o Several bugs were fixed in the code of all.equal.phylo().
1720 o Several bugs were fixed in write.dna(), particularly this
1721 function did not work with `format = "interleaved"'.
1723 o Various errors were corrected in the help pages.
1728 o The argument names of as.hclust.phylo() have been changed
1729 from "(phy)" to "(x, ...)" to conform to the definition of
1730 the corresponding generic function.
1732 o gamma.stat() has been renamed gammaStat() to avoid confusion
1733 since gamma() is a generic function.
1737 CHANGES IN APE VERSION 1.1-3
1742 o base.freq() previously did not return a value of 0 for
1743 bases absent in the data (e.g., a vector of length 3 was
1744 returned if one base was absent). This is now fixed (a
1745 vector of length 4 is always returned).
1747 o Several bugs were fixed in read.nexus(), including that this
1748 function did not work in this absence of a "TRANSLATE"
1749 command in the NEXUS file, and that the commands were
1754 CHANGES IN APE VERSION 1.1-2
1759 o The Tamura and Nei (1993) model of DNA distance is now implemented
1760 in dist.dna(): five models are now available in this function.
1762 o A new data set is included: a set of 15 sequences of the
1763 cytochrome b mitochondrial gene of the woodmouse (Apodemus
1769 o A bug in read.nexus() was fixed.
1771 o read.dna() previously did not work correctly in most cases.
1772 The function has been completely re-written and its help page
1773 has been considerably extended (see ?read.dna for details).
1774 Underscores (_) in taxon names are no more replaced with
1775 spaces (this behaviour was undocumented).
1777 o A bug was fixed in write.dna().
1781 CHANGES IN APE VERSION 1.1-1
1786 o A bug in read.tree() introduced in APE 1.1 was fixed.
1788 o A bug in compar.gee() resulted in an error when trying to fit
1789 a model with `family = "binomial"'. This is now fixed.
1793 CHANGES IN APE VERSION 1.1
1798 o The Klastorin (1982) method as suggested by Misawa and Tajima
1799 (2000, Mol. Biol. Evol. 17:1879-1884) for classifying genes
1800 on the basis of phylogenetic trees has been implemented (see
1801 the function klastorin()).
1803 o Functions have been added to convert APE's "phylo" objects in
1804 "hclust" cluster objects and vice versa (see the help page of
1805 as.phylo for details).
1807 o Three new functions, ratogram(), chronogram() and NPRS.criterion(),
1808 are introduced for the estimation of absolute evolutionary rates
1809 (ratogram) and dated clock-like trees (chronogram) from
1810 phylogenetic trees using the non-parametric rate smoothing approach
1811 by MJ Sanderson (1997, Mol. Biol. Evol. 14:1218-1231).
1813 o A summary method is now provided printing a summary information on a
1814 phylogenetic tree with, for instance, `summary(tree)'.
1816 o The behaviour of read.tree() was changed so that all spaces and
1817 tabulations in tree files are now ignored. Consequently, spaces in tip
1818 labels are no more allowed. Another side effect is that read.nexus()
1819 now does not replace the underscores (_) in tip labels with spaces
1820 (this behaviour was undocumented).
1822 o The function plot.phylo() has a new option (`underscore') which
1823 specifies whether the underscores in tip labels should be written on
1824 the plot as such or replaced with spaces (the default).
1826 o The function birthdeath() now computes 95% confidence intervals of
1827 the estimated parameters using profile likelihood.
1829 o Three new data sets are included: a gene tree estimated from 36
1830 landplant rbcL sequences, a gene tree estimated from 32 opsin
1831 sequences, and a gene tree for 50 BRCA1 mammalian sequences.
1836 o A bug was fixed in dist.gene() where nothing was returned.
1838 o A bug in plot.mst() was fixed.
1840 o A bug in vcv.phylo() resulted in false correlations when the
1841 option `cor = TRUE' was used (now fixed).
1845 CHANGES IN APE VERSION 1.0
1850 o Two new functions, read.dna() and write.dna(), read/write in a file
1851 DNA sequences in interleaved or in sequential format.
1853 o Two new functions, read.nexus() and write.nexus(), read/write trees
1856 o The new function bind.tree() allows to bind two trees together,
1857 possibly handling root edges to give internal branches.
1859 o The new function drop.tip() removes the tips in a phylogenetic tree,
1860 and trims (or not) the corresponding internal branches.
1862 o The new function is.ultrametric() tests if a tree is ultrametric.
1864 o The function plot.phylo() has more functionalities such as drawing the
1865 branches with different colours and/or different widths, showing the
1866 node labels, controling the position and font of the labels, rotating
1867 the labels, and controling the space around the plot.
1869 o The function read.tree() can now read trees with no branch length,
1870 such as "(a,b),c);". Consequently, the element `edge.length' in
1871 objects of class "phylo" is now optional.
1873 o The function write.tree() has a new default behaviour: if the default
1874 for the option `file' is used (i.e. file = ""), then a variable of
1875 mode character containing the tree in Newick format is returned which
1876 can thus be assigned (e.g., tree <- write.tree(phy)).
1878 o The function read.tree() has a new argument `text' which allows
1879 to read the tree in a variable of mode character.
1881 o A new data set is included: the phylogenetic relationships among
1882 the orders of birds from Sibley and Ahlquist (1990).
1886 CHANGES IN APE VERSION 0.2-1
1891 o Several bugs were fixed in the help pages.
1895 CHANGES IN APE VERSION 0.2
1900 o The function write.tree() writes phylogenetic trees (objects of class
1901 "phylo") in an ASCII file using the Newick parenthetic format.
1903 o The function birthdeath() fits a birth-death model to branching times
1904 by maximum likelihood, and estimates the corresponding speciation and
1907 o The function scale.bar() adds a scale bar to a plot of a phylogenetic
1910 o The function is.binary.tree() tests whether a phylogeny is binary.
1912 o Two generic functions, coalescent.intervals() and collapsed.intervals(),
1913 as well as some methods are introduced.
1915 o Several functions, including some generics and methods, for computing
1916 skyline plot estimates (classic and generalized) of effective
1917 population size through time are introduced and replace the function
1918 skyline.plot() in version 0.1.
1920 o Two data sets are now included: the phylogenetic relationships among
1921 the families of birds from Sibley and Ahlquist (1990), and an
1922 estimated clock-like phylogeny of HIV sequences sampled in the
1923 Democratic Republic of Congo.
1926 DEPRECATED & DEFUNCT
1928 o The function skyline.plot() in ape 0.1 has been deprecated and
1929 replaced by more elaborate functions (see above).
1934 o Two important bugs were fixed in plot.phylo(): phylogenies with
1935 multichotomies not at the root or not with only terminal branches,
1936 and phylogenies with a single node (i.e. only terminal branches)
1937 did not plot. These trees should be plotted correctly now.
1939 o Several bugs were fixed in diversi.time() in the computation of
1942 o Various errors were corrected in the help pages.
projects / ape.git / blob