X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=57a418c6ccc6900c31d67a1e6dab4f121120cda2;hb=06e83c6878153f8e7999c0470263c40aad4db258;hp=c702b68074489aa961044ce2efd6819da03b96c4;hpb=57296547225ce8a75813a996722c081da7837a88;p=ape.git diff --git a/NEWS b/NEWS index c702b68..57a418c 100644 --- a/NEWS +++ b/NEWS @@ -1,11 +1,201 @@ + CHANGES IN APE VERSION 3.0-1 + + +NEW FEATURES + + o dist.dna() has two new models: "indel" and "indelblock". + + o bind.tree() now accepts 'position' > 0 when the trees have no + banch length permitting to create a node in 'x' when grafting + 'y' (see ?bind.tree for details). + + +BUG FIXES + + o cophyloplot( , rotate = TRUE) made R hanged after a few clicks. + Also the tree is no more plotted twice. + + o read.GenBank() has been updated to work with EFetch 2.0. + + + + CHANGES IN APE VERSION 3.0 + + +NEW FEATURES + + o The three functions dyule, dbd, and dbdTime calculate the + density probability (i.e., the distribution of the number of + species) for the Yule, the constant and the time-dependent + birth-beath models, respectively. These probabilities can be + conditional on no extinction and/or on a log-scale. + + o plot.phylo() has a new option 'rotate.tree' to rotate unrooted, + fan, or radial trees around the center of the plot. + + o boot.phylo() and prop.clades() have a new option rooted = + FALSE. Note that the behaviour of prop.part() is unchanged. + + o edgelabels() has a new option 'date' to place labels on edges of + chronograms using the time scale (suggestion by Rob Lanfear). + + +BUG FIXES + + o In chronopl(), the code setting the initial dates failed in + complicated settings (several dates known within intervals). + This has been generally improved and should result in faster + and more efficient convergence even in simple settings. + + o mantel.test() sometimes returned P-values > 1 with the default + two-tailed test. + + o extract.clade() sometimes shuffled some tip labels (thanks to + Ludovic Mallet and Mahendra Mariadassou for the fix). + + o clustal() should now find by default the executable under Windows. + + +OTHER CHANGES + + o The code of yule() has been simplified and is now much faster for + big trees. + + o The code of mantel.test() has been adjusted to be consistent + with common permutation tests. + + o The C code of base.freq() has been improved and is now nearly 8 + times faster. + + o The option 'original.data' of write.nexus() is now deprecated and + will be removed in a future release. + + o The code of is.ultrametric() has been improved and is now 3 times + faster. + + o The code of vcv.phylo() has been improved and is now 10 or 30 + times faster for 100 or 1000 tips, respectively. Consequently, + fitting models with PGLS will be faster overall. + + + + CHANGES IN APE VERSION 2.8 + + +NEW FEATURES + + o Twelve new functions have been written by Andrei-Alin Popescu: + additive, ultrametric, is.compatible, arecompatible, mvr, mvrs, + njs, bionjs, SDM, treePop, triangMtd, triangMtd*. + + o A new class "bitsplits" has been created by Andrei-Alin Popescu + to code splits (aka, bipartition). + + o There is a new generic function as.bitsplits with a method to + convert from the class "prop.part" to the class "bitsplits". + + o The new function ltt.coplot plots on the same scales a tree and + the derived LTT plot. + + o ltt.plot() has two new options: backward and tol. It can now + handle non-ultrametic trees and its internal coding has been + improved. The coordinates of the plot can now be computed with + the new function ltt.plot.coords. + + +BUG FIXES + + o prop.part() crashed if some trees had some multichotomies. + + + + CHANGES IN APE VERSION 2.7-3 + + +NEW FEATURES + + o The new function compute.brtime computes and sets branching times. + + o mantel.test() has a new argument 'alternative' which is + "two-sided" by default. Previously, this test was one-tailed + with no possibility to change. + + o ace() can now do REML estimation with continuous characters, + giving better estimates of the variance of the Brownian motion + process. + + +BUG FIXES + + o Branch lengths were wrongly updated with bind.tree(, where = , + position = 0). (Thanks to Liam Revell for digging this bug out.) + + o Simulation of OU process with rTraitCont() did not work correctly. + This now uses formula from Gillespie (1996) reduced to a BM + process when alpha = 0 to avoid division by zero. The option + 'linear' has been removed. + + o Cross-validation in chronopl() did not work when 'age.max' was + used. + + o consensus(, p = 0.5) could return an incorrect tree if some + incompatible splits occur in 50% of the trees (especially with + small number of trees). + + o c() with "multiPhylo" did not work correctly (thanks to Klaus + Schliep for the fix). + + o root() failed in some cases with an outgroup made of several tips. + The help page has been clarified a bit. + + + CHANGES IN APE VERSION 2.7-2 NEW FEATURES - o plot.phylo() has a new option 'draw = TRUE'. If FALSE, the tree + o There is a new class "evonet" to code evolutionary networks, with + a constructor function evonet(), a print() and a plot() methods, + and four conversion methods to the classes "phylo", "networx", + "network", and "igraph". + + o The new function rTraitMult does multivariate traits simulation + with user-defined models. + + o plot.phylo() has a new option 'plot = TRUE'. If FALSE, the tree is not plotted but the graphical device is set and the - coordinates are saved as normal. + coordinates are saved as usual. + + o diversity.contrast.test() gains a fourth version of the test with + method = "logratio"; the literature citations have been clarified. + + o add.scale.bar() has two new options, 'lwd' and 'lcol', to modify + the aspect of the bar. + + o boot.phylo() now displays a progress bar by default (can be off + if 'quiet = TRUE'). + + o There is a new predict() method for compar.gee(). + + +BUG FIXES + + o bionj() made R crash if distances were too large. It now returns + an error if at least one distance is greater than 100. + + o drop.tip() returned a wrong tree if 'tip' was of zero length. + + o read.nexus.data() failed with URLs. + + o boot.phylo() returned overestimated support values in the + presence of identical or nearly identical sequences. + + +OTHER CHANGES + + o The data bird.families, bird.orders, cynipids, and woodmouse are + now provided as .rda files. @@ -40,8 +230,8 @@ BUG FIXES OTHER CHANGES - o identify.phylo() now returns NULL if the user right-(instead of - left-)clicks (an error was returned previously). + o identify.phylo() now returns NULL if the user right- (instead of + left-) clicks (an error was returned previously). o read.nexus() should be robust to commands inserted in the TREES block.