X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=e90cec15c61f7d4d1bae3e76033142edcfac8b3d;hb=2014b83971be4b9cd1644d6127837df798e9335c;hp=f80ec46d3747d4324a65594c83a0a90007da4800;hpb=29792fb8cef8ddab4553474398369fb6c24c1d8b;p=ape.git diff --git a/NEWS b/NEWS index f80ec46..e90cec1 100644 --- a/NEWS +++ b/NEWS @@ -1,9 +1,344 @@ + CHANGES IN APE VERSION 3.0-6 + + +NEW FEATURES + + o reorder.phylo() has a new order, "postorder", and a new option + index.only = TRUE to return only the vector of indices (the tree + is unmodified, see ?reorder.phylo for details). + + o The three new functions node.depth.edgelength, node.height, and + node.height.clado make some internal code available from R. See + ?node.depth (which was already documented) for details. + + +BUG FIXES + + o reorder(, "pruningwise") made R crash if the rows of the edge + matrix are in random order: this is now fixed. + + o drop.tip() sometimes shuffled node labels (thanks to Rebecca + Best for the report). + + o drop.tip(phy, "") returned a tree with zero-length tip labels: + it now returns the tree unchanged (thanks to Brian Anacker for + the report). + + o plot.phylo() made R crash if the tree has zero-length tip + labels: it now returns NULL (thanks again to Brian Anacker). + + +OTHER CHANGES + + o dist.nodes() is now 6 to 10 times faster. + + o reorder(, "cladewise") is now faster. The change is not very + visible for small trees (n < 1000) but this can be more than + 1000 faster for big trees (n >= 1e4). + + o The attribute "order" of the objects of class "phylo" is now + strongly recommended, though not mandatory. Most functions in + ape should return a tree with this attribute correctly set. + + o dbd() is now vectorized on both arguments 'x' (number of species + in clade) and 't' (clade age) to make likelihood calculations + easier and faster. + + + + CHANGES IN APE VERSION 3.0-5 + + +BUG FIXES + + o ace() should better catch errors when SEs cannot be computed. + + +OTHER CHANGES + + o write.dna(format = "fasta") now conforms more closely to the + FASTA standard thanks to François Michonneau. + + o print.DNAbin() does not print base compositions if there are more + than one million nucleotides. + + + + CHANGES IN APE VERSION 3.0-4 + + +BUG FIXES + + o read.dna() failed to read Phylip files if the first line used + tabulations instead of white spaces. + + o read.dna() failed to read Phylip or Clustal files with less than + 10 nucleotides. (See other changes in this function below.) + +OTHER CHANGES + + o read.dna() now requires at least one space (or tab) between the + taxa names and the sequences (whatever the length of taxa + names). write.dna() now follows the same rule. + + o The option 'seq.names' of read.dna has been removed. + + o The files ape-defunct.R and ape-defunct.Rd, which have not been + modified for almost two years, have been removed. + + o The C code of bionj() has been reworked: it is more stable (by + avoiding passing character strings), slightly faster (by about + 20%), and numerically more accurate. + + o The C code of fastme.*() has been slightly modified and should + be more stable by avoiding passing character strings (the + results are identical to the previous versions). + + o The file src/newick.c has been removed. + + + + CHANGES IN APE VERSION 3.0-3 + + +BUG FIXES + + o birthdeath() now catches errors and warnings much better so that + a result is returned in most cases. + + +OTHER CHANGES + + o Because of problems with character string manipulation in C, the + examples in ?bionj and in ?fastme have been disallowed. In the + meantime, these functions might be unstable. This will be solved + for the next release. + + + + CHANGES IN APE VERSION 3.0-2 + + +NEW FEATURES + + o The new function alex (alignment explorator) zooms in a DNA + alignment and opens the result in a new window. + + +BUG FIXES + + o compute.brtime() did not completely randomized the order of the + branching times. + + o write.nexus() did not work correctly with rooted trees (thanks + to Matt Johnson for the fix). + + o mltt.plot(, backward = FALSE) did not set the x-axis correctly. + + o A bug was introduced in prop.clades() with ape 3.0. The help page + has been clarified relative to the use of the option 'rooted'. + + o mantel.test() printed a useless warning message. + + o plot.phylo(, direction = "downward") ignored 'y.lim'. + + o is.monophyletic() did not work correctly if 'tips' was not stored + as integers. + + o prop.part() could make R crash if the first tree had many + multichotomies. + + o njs(), bionjs(), and mvrs() now return an error if 'fs < 1'. + + o SDM() did not work correctly. The code has also been generally + improved. + + +OTHER CHANGES + + o The DESCRIPTION file has been updated. + + o The option 'original.data' of write.nexus() has been removed. + + o The files bionjs.c, mvr.c, mvrs.c, njs.c, triangMtd.c, and + triangMtds.c have been improved which should fix some bugs in + the corresponding functions. + + o dist.gene() now coerces input data frame as matrix resulting in + much faster calculations (thanks to a suggestion by Markus + Schlegel). + + + + 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. + + o unroot() on trees in "pruningwise" order did not respect this + attribute. + + + + 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 usual. @@ -13,6 +348,11 @@ NEW FEATURES 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 @@ -23,6 +363,15 @@ BUG FIXES 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. + CHANGES IN APE VERSION 2.7-1 @@ -56,8 +405,8 @@ 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.