X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=NEWS;h=6c871841b94dba7d480bd99264ea9c43de64b3a3;hb=f5c4abe6ac31486e821d82788bf66b5db2be51d1;hp=6d74722e49d33a07139128b1f6bb68be65f6e75e;hpb=1df144a18356d9b329324324bc2f78cfdf1cea3d;p=ape.git diff --git a/NEWS b/NEWS index 6d74722..6c87184 100644 --- a/NEWS +++ b/NEWS @@ -1,19 +1,144 @@ + 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. + + o collapse.singles() is faster thanks to Klaus Schliep. This will + speed-up drop.tip() significantly. + + + + 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 interleaved files if the first line - uses tabulations instead of white spaces. + 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 more accurate numerically. + 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 @@ -361,7 +486,7 @@ 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. @@ -1903,14 +2028,14 @@ 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. @@ -1974,7 +2099,7 @@ 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'.