X-Git-Url: https://git.donarmstrong.com/?p=ape.git;a=blobdiff_plain;f=NEWS;h=807a2e4fe3fc37650dc74b45bb914126c94cb59a;hp=223169c57b1ff73d0570cb0d5c62f033d8900881;hb=HEAD;hpb=d1546ec66ff1a8ea123adefebe14f6316c23705f diff --git a/NEWS b/NEWS index 223169c..807a2e4 100644 --- a/NEWS +++ b/NEWS @@ -1,14 +1,326 @@ - CHANGES IN APE VERSION 2.8-1 + 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 mantel.test() could return P-values > 1 with the default + 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 @@ -18,6 +330,19 @@ OTHER CHANGES 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 @@ -171,8 +496,8 @@ 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. @@ -202,7 +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. @@ -1744,14 +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. @@ -1815,7 +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'.