X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=4307766a663a759649a47b851e476a317503c5a2;hb=c488b74490ee3d9d200de0e471881f002a18fe4f;hp=46af03fc06ef1fcf9e8a61d37760c26251265397;hpb=fb6a06e39b9c580b39c76fd95e950144e818f45d;p=ape.git diff --git a/NEWS b/NEWS index 46af03f..4307766 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,90 @@ + CHANGES IN APE VERSION 3.0-8 + + +NEW FEATURES + + o The new function ewLasso whether tests an incomplete set of + distances uniquely determines the edge weights of a given + unrooted topology using the 'Lasso' method by Dress et + al. (2012, J. Math. Biol. 65:77). + + o ace() gains a new option 'use.expm' to use expm() from the + package of the same name in place of matexpo(). + + +BUG FIXES + + o read.dna(, "fasta") may add '\r' in labels: this is fixed. + + o prop.clades() returned wrong numbers when the tip labels of + 'phy' are not in the same order than the list of trees (thanks + to Rupert Collins for the report). + + o CADM.post() displayed "1" on the diagonal of the matrix of + Mantel p-values. It now displays "NA" on the diagonal, + indicating that no test of significance is computed between a + distance matrix and itself. + + +OTHER CHANGES + + o The files CDAM.global.R and CDAM.post.R have been renamed + CADM.global.R and CADM.post.R. + + o ace() has a new default for its option 'method': this is "REML" + for continuous characters and "ML" for discrete ones. + + o ape now imports the package expm so this one must be installed. + + + + CHANGES IN APE VERSION 3.0-7 + + +NEW FEATURES + + o The new function chronos estimates chronograms by penalised + likelihood and maximum likelihood with a completely reworked + code and interface. There is a new function makeChronosCalib to + set the calibration points easily. chronos() will eventually + replace chronopl(). + + o The new function 'where' searches patterns in DNA sequences. + + o pic() gains an option 'rescaled.tree = FALSE' to return the tree + with its branch lengths rescaled for the PIC calculation. + + o clustal(), muscle(), and tcoffee() gain an option + 'original.ordering = TRUE' to ease the comparisons of + alignments. + + o plot.phylo() has a new option, open.angle, used when plotting + circular trees. + + o The new function read.FASTA reads FASTA files much faster and + more efficiently. It is called internally by read.dna(, "fasta") + or can be called directly. + + +BUG FIXES + + o drop.tip() shuffled node labels on some trees. + + o axisPhylo() now works correctly with circular trees, and gives a + sensible error message when type = "r" or "u". + + +OTHER CHANGES + + o .compressTipLabel() is 10 times faster thanks to Joseph Brown. + + o base.freq() is now faster with lists. + + o as.matrix.DNAbin() should be faster and more efficient with + lists; it now accepts vectors. + + + CHANGES IN APE VERSION 3.0-6 @@ -5,13 +92,27 @@ 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). + 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. + 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 @@ -22,6 +123,14 @@ OTHER CHANGES 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 @@ -414,7 +523,7 @@ NEW FEATURES o base.freq() gains an option 'all' to count all the possible bases including the ambiguous ones (defaults to FALSE). - o read.nexus() now writes tree names in the NEXUS file if given a + o write.nexus() now writes tree names in the NEXUS file if given a list of trees with names. @@ -1956,14 +2065,14 @@ BUG FIXES o A bug was fixed in phymltest(): the executable couldn't be found in some cases. - o Three bug have been fixed in ace(): computing the likelihood of + o Three bugs have been fixed in ace(): computing the likelihood of ancestral states of discrete characters failed, custom models did not work, and the function failed with a null gradient (a warning message is now returned; this latter bug was also present in yule.cov() as well and is now fixed). - o pic() hanged out when missing data were present: a message error - is now returned. + o pic() hanged out when missing data were present: an error is now + returned. o A small bug was fixed in dist.dna() where the gamma correction was not always correctly dispatched. @@ -2027,7 +2136,7 @@ NEW FEATURES DNA sequences by specifying model = "raw". o dist.phylo() has a new option `full' to possibly compute the - distances among all tips and nodes of the tree. The default if + distances among all tips and nodes of the tree. The default is `full = FALSE'.