X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=df3b32bc4fd721ecdac92e35d283d1c2b09e506b;hb=82dd3702485179ba5408f1e3e57eb856d025e16c;hp=678bba7b17c60151cf7e1dd0924e69c7ae72341e;hpb=f512087dd94a7dc3462a9f31b48f61214cdc0f5e;p=ape.git diff --git a/ChangeLog b/ChangeLog index 678bba7..df3b32b 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,9 +1,301 @@ + CHANGES IN APE VERSION 2.5-4 + + +NEW FEATURES + + 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. + + + + 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 + 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'. @@ -140,7 +432,7 @@ BUG FIXES OTHER CHANGES - o There is now a general help page displayed with '?ape' + o There is now a general help page displayed with '?ape'. @@ -175,7 +467,7 @@ OTHER CHANGES o ape has now a namespace. - o drip.tip() has been improved: it should be much faster and work + o drop.tip() has been improved: it should be much faster and work better in some cases (e.g., see the example in ?zoom). @@ -1093,6 +1385,8 @@ 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.