X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=a635615eecbe29422c094b6ce0daee4177b9e068;hb=453ad4ce9e573998f28185d92c8d71367dd32f23;hp=600e598bc667f1603115ef305a440cdc8900ca2f;hpb=15e231b55ef0be61c20bfc82efd2316e085122a9;p=ape.git diff --git a/ChangeLog b/ChangeLog index 600e598..a635615 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,331 @@ + CHANGES IN APE VERSION 2.6-4 + + +NEW FEATURES + + o There is a new image() method for "DNAbin" objects: it plots DNA + alignments in a flexible and efficient way. + + o Two new functions as.network.phylo and as.igraph.phylo convert + trees of class "phylo" into these respective network classes + defined in the packages of the same names. + + o The three new functions clustal, muscle, and tcoffee perform + nucleotide sequence alignment by calling the external programs + of the same names. + + o base.freq() gains an option 'all' to count all the possible bases + including the ambiguous ones (defaults to FALSE). + + o read.nexus() now writes tree names in the NEXUS file if given a + list of trees with names. + + +BUG FIXES + + o prop.part() failed in some situations with unrooted trees. + + o read.nexus() shuffled node labels when a TRANSLATE block was + present. + + o varCompPhylip() did not work if 'exec' was specified. + + o bind.tree() shuffled node labels when position > 0 and 'where' + was not the root. + + +OTHER CHANGES + + o BaseProportion in src/dist_dna.c has been modified. + + o A number of functions in src/tree_build.c have been modified. + + o The matching representation has now only two columns as the third + column was redundant. + + + + CHANGES IN APE VERSION 2.6-3 + + +NEW FEATURES + + o rTraitCont() and rTraitDisc() gains a '...' argument used with + user-defined models (suggestion by Gene Hunt). + + +BUG FIXES + + o as.hclust.phylo() now returns an error with unrooted trees. + + o as.hclust.phylo() failed with trees with node labels (thanks to + Jinlong Zhang for pointing this bug out). + + o read.dna(, "fasta") failed if sequences were not all of the same + length. + + o plot.phylo() did not recycle values of 'font', 'cex' and + 'tip.color' correctly when type = "fan" or "radial". + + o plot.phylo() ignored 'label.offset' when type = "radial", "fan", or + "unrooted" with lab4ut = "axial" (the placement of tip labels still + needs to be improved with lab4ut = "horizontal"). + + +OTHER CHANGES + + o In drop.fossil() the default tol = 0 has been raised to 1e-8. + + o The help command ?phylo now points to the man page of read.tree() + where this class is described. Similarly, ?matching points to the + man page of as.matching(). + + + + 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 and Jeremy Beaulieu for the fix). + + o ace(type = "discrete") has been improved thanks to Naim Marasci and + Jeremy Beaulieu. + + + + 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 @@ -5,8 +333,11 @@ 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. + 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. @@ -14,10 +345,21 @@ NEW FEATURES 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 @@ -28,6 +370,12 @@ BUG FIXES 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 @@ -1231,6 +1579,8 @@ 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.