X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=600e598bc667f1603115ef305a440cdc8900ca2f;hb=15e231b55ef0be61c20bfc82efd2316e085122a9;hp=2d14a5ba3a3332a55185379fde7d3eaf19533bc7;hpb=bea9a4387337eaa1990123745315eb04a1759fc9;p=ape.git diff --git a/ChangeLog b/ChangeLog index 2d14a5b..600e598 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,228 @@ + 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 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 add.scale.bar() has a new option 'ask' to draw interactively. + + o The branch length score replaces the geodesic distance in dist.topo. + + +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). + + + + 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 @@ -10,6 +235,35 @@ NEW FEATURES 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 @@ -24,7 +278,7 @@ 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'. @@ -59,7 +313,7 @@ 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).