X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=807a2e4fe3fc37650dc74b45bb914126c94cb59a;hb=refs%2Fheads%2Fmaster;hp=812bb6c414cdbf2a9e8f3b54bbbb63b0e711c441;hpb=2653eb671caf9234635e44b895ef48b377a89a78;p=ape.git diff --git a/NEWS b/NEWS index 812bb6c..807a2e4 100644 --- a/NEWS +++ b/NEWS @@ -1,6 +1,124 @@ + CHANGES IN APE VERSION 3.0-8 + + +NEW FEATURES + + o The new function ewLasso tests whether 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. + + o rtree(n, rooted = FALSE) returned trees with an 'edge' matrix + stored as doubles instead of integers for n > 4. + + +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 does not import gee anymore so the latter doesn't need to + 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 +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. @@ -9,6 +127,14 @@ 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 @@ -401,7 +527,7 @@ 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. @@ -1943,14 +2069,14 @@ 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. @@ -2014,7 +2140,7 @@ 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'.