X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=5e2a0fadeb08e215ea684f3ff9ec397d04286b3d;hb=92ef6853c5cb0e730dad1af9961064239a1d375f;hp=61c911f870229067309416c0a28452b36005b004;hpb=1090d5990d4b6f7feb10c87638f4229f53891eb7;p=ape.git diff --git a/ChangeLog b/ChangeLog index 61c911f..5e2a0fa 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,181 @@ + CHANGES IN APE VERSION 2.5-4 + + +NEW FEATURES + + o There is now an 'as.list' method for the class "DNAbin". + + + + 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 @@ -34,6 +212,9 @@ BUG FIXES 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 @@ -1197,6 +1378,8 @@ 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.