X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=057cf583a570dd78448d2e318059d3aaadd33e53;hb=081bbd65bc9bbf19658c1dfc0724d17bf925626e;hp=e2fc4cec9a3872f837ceb004644c41632ccec0ac;hpb=f820fadc890587f8a3499f96b07b99fa80fc62ab;p=ape.git diff --git a/ChangeLog b/ChangeLog index e2fc4ce..057cf58 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,584 @@ + CHANGES IN APE VERSION 2.6-2 + + +NEW FEATURES + + o Two new functions, pic.ortho and varCompPhylip, implements the + orthonormal contrasts of Felsenstein (2008, Am Nat, 171:713). The + second function requires Phylip to be installed on the computer. + + o bd.ext() has a new option conditional = TRUE to use probabilities + conditioned on no extinction for the taxonomic data. + + +BUG FIXES + + o write.tree() failed to output correctly tree names. + + o dist.nodes() returned duplicated column(s) with unrooted and/or + multichotomous trees. + + o mcmc.popsize() terminated unexpectedly if the progress bar was + turned off. + + o prop.part(x) made R frozen if 'x' is of class "multiPhylo". + + o Compilation under Mandriva failed (thanks to Jos Käfer for the fix). + + o drop.tip() shuffled tip labels with subtree = TRUE or trim.internal + = FALSE. + + o Objects returned by as.hclust.phylo() failed when analysed with + cutree() or rect.hclust(). + + o write.tree() did not output correctly node labels (thanks to Naim + Matasci for the fix). + + + + CHANGES IN APE VERSION 2.6-1 + + +NEW FEATURES + + o The new function speciesTree calculates the species tree from a set + of gene trees. Several methods are available including maximum tree + and shallowest divergence tree. + + +BUG FIXES + + o A bug introduced in write.tree() with ape 2.6 has been fixed. + + o as.list.DNAbin() did not work correctly with vectors. + + o as.hclust.phylo() failed with trees with node labels (thanks to + Filipe Vieira for the fix). + + + + CHANGES IN APE VERSION 2.6 + + +NEW FEATURES + + o The new functions rlineage and rbdtree simulate phylogenies under + any user-defined time-dependent speciation-extinction model. They + use continuous time algorithms. + + o The new function drop.fossil removes the extinct species from a + phylogeny. + + o The new function bd.time fits a user-defined time-dependent + birth-death model. It is a generalization of yule.time() taking + extinction into account. + + o The new function MPR does most parsimonious reconstruction of + discrete characters. + + o The new function Ftab computes the contingency table of base + frequencies from a pair of sequences. + + o There is now an 'as.list' method for the class "DNAbin". + + o dist.dna() can compute the number of transitions or transversions + with the option model = "Ts" or model = "Tv", respectively. + + o [node|tip|edge]labels() gain three options with default values to + control the aspect of thermometers: horiz = TRUE, width = NULL, + and height = NULL. + + o compar.gee() has been improved with the new option 'corStruct' as an + alternative to 'phy' to specify the correlation structure, and + calculation of the QIC (Pan 2001, Biometrics). The display of the + results has also been improved. + + o read.GenBank() has a new option 'gene.names' to return the name of + the gene (FALSE by default). + + +BUG FIXES + + o extract.clade() sometimes shuffled the tip labels. + + o plot.phylo(type = "unrooted") did not force asp = 1 (thanks to Klaus + Schliep for the fix) + + o dist.dna(model = "logdet") used to divide distances by 4. The + documentation has been clarified on the formulae used. + + +OTHER CHANGES + + o rTraitCont(model = "OU") has an option 'linear = TRUE' to possibly + change the parameterisation (see ?rTraitCont for details). + + o pic() now returns a vector with the node labels of the tree (if + available) as names. + + o write.tree() and read.tree() have been substantially improved thanks + to contributions by Klaus Schliep. + + + + CHANGES IN APE VERSION 2.5-3 + + +NEW FEATURES + + o The new function mixedFontLabel helps to make labels with bits of + text to be plotted in different fonts. + + o There are now replacement operators for [, [[, and $ for the class + "multiPhylo" (i.e., TREES[11:20] <- rmtree(10, 100)). They possibly + check that the tip labels are the same in all trees. + + o Objects of class "multiPhylo" can be built with c(): there are + methods for the classes "phylo" and "multiPhylo". + + o The internal functions .compressTipLabel and .uncompressTipLabel are + now documented. + + +BUG FIXES + + o bind.tree(x, y, where, position = 0) did not work correctly if 'y' + was a single-edge tree and 'where' was a tip. + + o rTraitCont() did not use the square-root of branch lengths when + simulating a Brownian motion model. + + + + CHANGES IN APE VERSION 2.5-2 + + +NEW FEATURES + + o There is now a print method for results from ace(). + + o There is a labels() method for objects of class "DNAbin". + + o read.dna() has a new option 'as.matrix' to possibly force sequences + in a FASTA file to be stored in a matrix (see ?read.dna for details). + + +BUG FIXES + + o as.phylo.hclust() used to multiply edge lengths by 2. + + o A minor bug was fixed in rTraitDisc(). + + o ace() sometimes failed (parameter value was NaN and the optimisation + failed). + + +DEPRECATED & DEFUNCT + + o evolve.phylo() and plot.ancestral() have been removed. + + o chronogram(), ratogram(), and NPRS.criterion() have been removed. + + +OTHER CHANGES + + o nj() has been improved and is now about 30% faster. + + o The default option 'drop' of [.DNAbin has been changed to FALSE to + avoid dropping rownames when selecting a single sequence. + + o print.DNAbin() has been changed to summary.DNAbin() which has been + removed. + + + + CHANGES IN APE VERSION 2.5-1 + + +NEW FEATURES + + o The new function stree generates trees with regular shapes. + + o It is now possible to bind two trees with x + y (see ?bind.tree for + details). + + o drop.tip(), extract.clade(), root(), and bind.tree() now have an + 'interactive' option to make the operation on a plotted tree. + + o cophyloplot() gains two new arguments 'lwd' and 'lty' for the + association links; they are recycled like 'col' (which wasn't before). + + +BUG FIXES + + o rTraitDisc() did not use its 'freq' argument correctly (it was + multiplied with the rate matrix column-wise instead of row-wise). + + o [node|tip|edge]labels(thermo = ) used to draw empty thermometers + with NA values. Nothing is drawn now like with 'text' or 'pch'. + The same bug occurred with the 'pie' option. + + o A bug was fixed in compar.ou() and the help page was clarified. + + o bind.tree() has been rewritten fixing several bugs and making it + more efficient. + + o plot.phylo(type = "p") sometimes failed to colour correctly the + vertical lines representing the nodes. + + o plot.phylo(direction = "l", x.lim = 30) failed to plot the branches + in the correct direction though the tip labels were displayed + correctly. + + +OTHER CHANGES + + o The c, cbind, and rbind methods for "DNAbin" objetcs now check that + the sequences are correctly stored (in a list for c, in a matrix + for the two other functions). + + + + CHANGES IN APE VERSION 2.5 + + +NEW FEATURES + + o The new function parafit by Pierre Legendre tests for the + coevolution between hosts and parasites. It has a companion + function, pcoa, that does principal coordinate decomposition. + The latter has a biplot method. + + o The new function lmorigin by Pierre Legendre performs multiple + regression through the origin with testing by permutation. + + o The new functions rTraitCont and rTraitDisc simulate continuous and + discrete traits under a wide range of evolutionary models. + + o The new function delta.plot does a delta plot following Holland et + al. (2002, Mol. Biol. Evol. 12:2051). + + o The new function edges draws additional branches between any nodes + and/or tips on a plotted tree. + + o The new function fancyarrows enhances arrows from graphics with + triangle and harpoon heads; it can be called from edges(). + + o add.scale.bar() has a new option 'ask' to draw interactively. + + o The branch length score replaces the geodesic distance in dist.topo. + + o Three new data sets are included: the gopher-lice data (gopher.D), + SO2 air pollution in 41 US cities (lmorigin.ex1, from Sokal & + Rohlf 1995), and some host-parasite specificity data + (lmorigin.ex2, from Legendre & Desdevises 2009). + + +BUG FIXES + + o add.scale.bar() drew the bar outside the plotting region with the + default options with unrooted or radial trees. + + o dist.topo() made R stuck when the trees had different sizes (thanks + to Otto Cordero for the fix). + + +OTHER CHANGES + + o The geodesic distance has been replaced by the branch length score + in dist.topo(). + + + + CHANGES IN APE VERSION 2.4-1 + + +NEW FEATURES + + o rtree() and rcoal() now accept a numeric vector for the 'br' + argument. + + o vcv() is a new generic function with methods for the classes "phylo" + and "corPhyl" so that it is possible to calculate the var-cov matrix + for "transformation models". vcv.phylo() can still be used for trees + of class "phylo"; its argument 'cor' has been renamed 'corr'. + + +BUG FIXES + + o bind.tree() failed when 'y' had no root edge. + + o read.nexus() shuffled tip labels when the trees have no branch + lengths and there is a TRANSLATE block. + + o read.nexus() does not try to translate node labels if there is a + translation table in the NEXUS file. See ?read.nexus for a + clarification on this behaviour. + + o plot.multiPhylo() crashed R when plotting a list of trees with + compressed tip labels. + + o write.nexus() did not translate the taxa names when asked for. + + o plot.phylo(type = "fan") did not rotate the tip labels correctly + when the tree has branch lengths. + + o ace(type = "continuous", method = "ML") now avoids sigma² being + negative (which resulted in an error). + + o nj() crashed with NA/NaN in the distance matrix: an error in now + returned. + + + + CHANGES IN APE VERSION 2.4 + + +NEW FEATURES + + o base.freq() has a new option 'freq' to return the counts; the + default is still to return the proportions. + + +BUG FIXES + + o seg.sites() did not handle ambiguous nucleotides correctly: they + are now ignored. + + o plot(phy, root.edge = TRUE) failed if there was no $root.edge in + the tree: the argument is now ignored. + + o add.scale.bar() failed when 'x' and 'y' were given (thanks to Janet + Young for the fix). + + +OTHER CHANGES + + o Trying to plot a tree with a single tip now returns NULL with a + warning (it returned an error previously). + + o The way lines representing nodes are coloured in phylograms has + been modified (as well as their widths and types) following some + users' request; this is only for dichotomous nodes. + + o The argument 'adj' in [node][tip][edge]labels() now works when + using 'pie' or 'thermo'. + + o A more informative message error is now returned by dist.dna() when + 'model' is badly specified (partial matching of this argument is + done now). + + o Deprecated functions are now listed in a help page: see + help("ape-defunct") with the quotes. + + +DEPRECATED & DEFUNCT + + o The functions heterozygosity, nuc.div, theta.h, theta.k and + theta.s have been moved from ape to pegas. + + o The functions mlphylo, DNAmodel and sh.test have been removed. + + + + CHANGES IN APE VERSION 2.3-3 + + +BUG FIXES + + o add.scale.bar() always drew a horizontal bar. + + o zoom() shuffled tips with unrooted trees. + + o write.nexus() failed to write correctly trees with a "TipLabel" + attribute. + + o rcoal() failed to compute branch lengths with very large n. + + o A small bug was fixed in compar.cheverud() (thanks to Michael + Phelan for the fix). + + o seg.sites() failed when passing a vector. + + o drop.tip() sometimes shuffled tip labels. + + o root() shuffled node labels with 'resolve.root = TRUE'. + + + + CHANGES IN APE VERSION 2.3-2 + + +BUG FIXES + + o all.equal.phylo() did not compare unrooted trees correctly. + + o dist.topo(... method = "PH85") did not treat unrooted trees + correctly (thanks to Tim Wallstrom for the fix). + + o root() sometimes failed to test for the monophyly of the + outgroup correctly. + + o extract.clade() sometimes included too many edges. + + o vcv.phylo() did not work correctly when the tree is in + "pruningwise" order. + + o nj() did not handle correctly distance matrices with many 0's. + The code has also been significantly improved: 7, 70, 160 times + faster with n = 100, 500, 1000, respectively. + + + + CHANGES IN APE VERSION 2.3-1 + + +NEW FEATURES + + o The new function is.monophyletic tests the monophyly of a group. + + o There is now a c() method for lists of class "DNAbin". + + o yule.cov() now fits the null model, and its help page has been + corrected with respect to this change. + + o drop.tip() has a new option 'rooted' to force (or not) a tree + to be treated as (un)rooted. + + +BUG FIXES + + o dist.gene() failed on most occasions with the default + pairwise.deletion = FALSE. + + o read.tree() failed to read correctly the tree name(s). + + o boot.phylo() now treats correctly data frames. + + o del.gaps() did not copy the rownames of a matrix. + + o A small bug was fixed in CDAM.global(). + + o ace() failed with large data sets. Thanks to Rich FitzJohn for + the fix. With other improvements, this function is now about 6 + times faster. + + o write.tree() failed with objects of class "multiPhylo". + + o drop.tip(, subtree = TRUE) sometimes shuffled tip labels. + + +OTHER CHANGES + + o [.multiPhylo and [.DNAbin now respect the original class. + + o Instances of the form class(phy) == "phylo" have been replaced + by inherits(phy, "phylo"). + + o rcoal() is now faster. + + +DEPRECATED & DEFUNCT + + o klastorin() has been removed. + + + + CHANGES IN APE VERSION 2.3 + + +NEW FEATURES + + o The new functions CADM.global and CADM.post, contributed by + Pierre Legendre, test the congruence among several distance + matrices. + + o The new function yule.time fits a user-defined time-dependent + Yule model by maximum likelihood. + + o The new function makeNodeLabel creates and/or modifies node + labels in a flexible way. + + o read.tree() and write.tree() have been modified so that they can + handle individual tree names. + + o plot.phylo() has a new argument 'edge.lty' that specifies the + types of lines used for the edges (plain, dotted, dashed, ...) + + o phymltest() has been updated to work with PhyML 3.0.1. + + +BUG FIXES + + o drop.tip() shuffled tip labels in some cases. + + o drop.tip() did not handle node.label correctly. + + o is.ultrametric() now checks the ordering of the edge matrix. + + o ace() sometimes returned negative values of likelihoods of + ancestral states (thanks to Dan Rabosky for solving this long + lasting bug). + + +OTHER CHANGES + + o The data set xenarthra has been removed. + + + + CHANGES IN APE VERSION 2.2-4 + +BUG FIXES + + o The bug fix in read.nexus() in version 2.2-3 was wrong: this is + now fixed. (Thanks to Peter Wragg for the fix!) + + o A warning message occurred for no reason with ace(method="GLS"). + + +OTHER CHANGES + + o There is now a general help page displayed with '?ape'. + + + + CHANGES IN APE VERSION 2.2-3 + + +NEW FEATURES + + o The new function extract.clade extracts a clade from a tree by + specifying a node number or label. + + o fastme.bal() has two new options 'spr' and 'tbr' to perform tree + operations of the same names. + + o dist.dna() can now return the number of site differences by + specifying model="N". + + +BUG FIXES + + o chronopl() did not work with CV = TRUE. + + o read.nexus() did not work correctly in some situations (trees on + multiple lines with different numbers of lines and/or with + comments inserted within the trees). + + o ltt.plot(), ltt.lines(), and mltt.plot() did not count correctly + the number of lineages with non-binary trees. + + +OTHER CHANGES + + o ape has now a namespace. + + o drop.tip() has been improved: it should be much faster and work + better in some cases (e.g., see the example in ?zoom). + + + CHANGES IN APE VERSION 2.2-2 @@ -911,6 +1492,8 @@ OTHER CHANGES o dist.taxo() has been renamed as weight.taxo(). + o dist.phylo() has been replaced by the method cophenetic.phylo(). + o Various error and warning messages have been improved.