X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=c551deda10ce5fdb401272ecfa8a214adc31d645;hb=90f18c75d642f56b020bc6e0cdd0c5949c1d9a1d;hp=efef3ba6cedea36dba17a9e51cb601bab081a324;hpb=7e78dcfcf1bca3d6aaca7ae92ab0f4fb3d9cc711;p=ape.git diff --git a/ChangeLog b/ChangeLog index efef3ba..c551ded 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,13 +1,242 @@ + 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. + + +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. + + + + 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 @@ -26,6 +255,10 @@ BUG FIXES 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 @@ -36,6 +269,9 @@ OTHER CHANGES o rcoal() is now faster. + +DEPRECATED & DEFUNCT + o klastorin() has been removed. @@ -95,7 +331,7 @@ 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'. @@ -130,7 +366,7 @@ 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). @@ -1048,6 +1284,8 @@ 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.